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"They have a big problem coming up," the zombie drama's new showrunner tells THR about the events of "Infected."

[Warning: This story contains spoilers from The Walking Dead's "Infected" episode.]

The survivors of The Walking Dead faced two new threats Sunday in the second episode of its fourth season, after Patrick, who succumbed to a flu and turned overnight, terrorized the gated community of the prison.

During the hour, Zombie Patrick attacks what used to be his own community, spreading both the flu (which seemingly has also taken out the pigs) and turning more members of the group into walkers. As for the source of the virus, that continues to remain a mystery -- as does just who is baiting the undead to the weakening gates of the prison.

The Hollywood Reporter caught up with showrunner Scott M. Gimple to dissect the episode.

The flu has spread to Karen -- does that narrow down the origins of the virus to either animals or water?

One thing I really dug about this story when we were talking about it [in the writers' room] is that because of the third-world situation that they're in -- it's almost medieval -- they don't get to know; they don't have a lab to take samples and look at stuff under microscopes. They need to roll with it and figure it out in a really difficult situation to do so. And the audience has to, too.

Carol (Melissa McBride) is now charged with caring for two young girls, Lizzie and Mika. What will she do differently after losing Sophia now that she's arming everyone?

She lost her daughter in a horrible way, and she absolutely got the memo regarding everything that happened with that. Carol was already teaching the children at the prison how to protect themselves at all costs to make sure that they don't become victims [like Sophia ultimately was]. With these two girls, she's going to continue that. It hits her now in a much deeper way -- these are her daughters now for all intents and purposes, and suddenly she's a mom again. She was pretty determined even before she was in that position, so it's only going to get more intense that way.

Mika, the younger of the sisters, reveals that Lizzie is "messed up, not weak." In the comics, Sophia grappled with sanity while she was at the prison. Is this a remix of her story with Carl?

Yes. There's a couple things going on there that's taking elements of various stories from the prison and elsewhere in the comic. In the comic, Sophia winds up essentially becoming Maggie's daughter. Kids wind up with other people in the comic. That was something that absolutely came from the comic. Yes, Sophia in the comic, after losing Carol, was not completely looking at the world the right way; she didn't even remember Carol very quickly in the comic, which happened at the farm. A lot of this stuff is subliminal. Having read the comic as much as I have, even after the fact, I realized something that Robert [Kirkman] did. One of my favorite covers of all-time of The Walking Dead was Carl and Sofia holding hands in front of the fences with the walkers. I'm sure that that influenced stuff in [episodes] 401 and 402. That contrast of innocence with threats and death -- there's a whole lot of remixing going on there.

The group is now divided between those who have been exposed to the flu, leaving Michonne (Danai Gurira), Maggie (Lauren Cohan) and Carl (Chandler Riggs) split from the rest of the group. How will that change the leadership within the prison?

The council is getting broken up, and all stability at the prison -- all these things that they built -- are being challenged and compromised. The momentum to this is not good for them holding on to what they have.

The group thinks someone is leaving mice near the fence -- which could be another threat from within their walls. How long can this group stay at the prison?

It looks like that might be what's going on; that's what they're speculating it is. They're going to be tested. The thing I love is that you find safety in this world. You find these walls, and then those walls start closing in on you. And what the hell do you then?

Someone is feeding rats to the walkers and drawing them to the fences of the prison. Could Bob (Larry Gilliard Jr.) be connected to this? We don't know much about him before Daryl brings him to the prison.

There's a lot of speculation online with that, and I shall not comment! But I will say that Bob does have a lot going on under the surface.

Michonne starts crying while holding Rick's baby, Judith. She was a mother in the comics. Could we see more of her backstory in flashbacks this year?

Michonne's story is very much tied in to finding out more about how she became who she is. One of my goals was to explore all of these characters to the nth-degree. Michonne has a lot of mystery about her. And as a reader of the comic and that Michonne one shot -- which wasn't in the comic -- and even a viewer of the show, I want to find out more about these characters, and I want to know how Michonne wound up the Michonne we know and love.

Why does Carl tell Rick (Andrew Lincoln) that Carol is teaching the kids how to defend themselves after she asked him not to?

He's his father's son, and that shows the strength of their relationship. Even though Carl did share this information, he also shared that he thought Rick should let her continue doing what she's doing. He did it with a recommendation and to maybe surprise this sad moment that Rick knows his son is right and that Carol is right. What we were shooting for was to see these two on the same page. Carl has not been totally down with the changes that have happened to his life and has moved away from being a soldier. But he is down with being his father's son; he appreciates that. To see Rick go toward Carl's line of thinking is a strong family moment for them.

Was there any part of that that was Carl manipulating Rick in order to get his gun back?

No way.

Considering the path that Carl was on at the end of season three when it was a question of whether he was going to be more like the Governor (David Morrissey) or his father, it seemed like it could have been in line with his dark leanings.

That's the goal: to show even though he still has that desire to be the soldier, he still wants to be his father's son and he wants to follow his dad's lead. There has been a change in Carl that Rick fostered that he enacted.

Rick (Andrew Lincoln) realizes he can't continue to take a back seat anymore and resumes carrying his holster and gun. How will he change going forward?

We started him off in a very peaceful place -- as peaceful as you can get on this show. He's achieved something for his family and for himself and the people around him. Clara said to him, "It's almost like a curse -- you don't get to come back from the things you've done." From the time he got back from there, that pig -- one of the symbols of what he achieved with his farm life -- had died. Things are getting taken away from him: There goes the farm, there's a gun in his son's hand, and he'd taken that gun out of his hand, and things are slowly being taken away from him. All the things he's achieved, he's going to be challenged whether he can hold on to them. Whether it's his identity, his family, his relationship to the people in the prison, it's all coming to a head very quickly.

The prison is very susceptible now to the walkers. How much longer can they stay there?

We've shown from the beginning that they have to do this regular maintenance on those fences -- meaning taking out walkers at fences. They're a little busy right now, and they're not at full strength but they need to be. They have a big problem coming up. We've talked about different locations this season, so who knows what can happen. Who knows, maybe they'll pull it off and maybe that requires another location. Maybe other locations come from them not pulling it off. It comes to a head sooner than later.

Tyreese finds Karen (Melissa Ponzio) has been killed and dragged outside, where her body -- and David, who was also sick -- were burned. Were these preventative slayings, or is someone targeting people who are sick with the flu?

Those were the two sickest people who were put away from everybody else. We also know some weird and scary things have been going on at the prison. So was it because they were sick? Was it because they were easy targets set away from everyone? I can only speculate along with you even though I totally know the answer (laughs).

It seems like there's a murder within the walls of the prison. Could whoever burned Karen's and David's bodies be the same person who is trying to force the group out of the prison from within? There's the origin of the flu, the rat bait at the fences …

Totally possible. Maybe, maybe not! It's a totally lame answer. But I will tell you this: It will be answered sooner rather than later.

Tyreese (Chad Coleman) had this peaceful approach to living in this world -- with Karen. How will her death change him?

That is a terrific question. We don't know Tyreese's full story, but the way he carries himself, he hasn't lost much the same way that some other people have since the turn. He hasn't lost his wife -- I'm not saying he had one -- but compared to Rick, he hasn't had these crushing losses. This is a very defining moment for him; it's his first big loss. Everybody has lost something, and everybody has lost this world, but for Tyreese, this is the first big loss he's had. It will change him, and it's going to deeply affect him. We're going to see those effects right at the start of the next episode.

Who do you think is behind the two slayings? Do you think the flu, fence bait and killings is the work of the same person? Hit the comments below with your thoughts. The Walking Dead airs Sundays at 9 p.m. on AMC.